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Old 06-14-2011, 07:16 AM   #1
madsaan
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Location: california

Join Date: Jan 2011
Posts: 26
Question BWA - sampe max occurrences of a read for pairing

Hello,

Can anyone explain what the parameter -o means for sampe.According to BWA manual it says "A read with more occurrences will be treated as a single-end read.Reducing this parameter helps faster pairing".

Does it mean uneven number of reads in the two input fastq files?How do you decide what parameter to use?

Any help will be greatly appreciated.

Thanks,
Joji
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